\(\renewcommand{\AA}{\text{Å}}\)

write_molecule command

Syntax

write_molecule mol-ID file

  • mol-ID = ID of the molecule template to be written

  • file = name of file to write the molecule template to

Examples

write_molecule mol1 molecule1.mol
write_molecule mol1 molecule1.json
write_molecule twomols template_set%.mol

Description

Added in version TBD.

Write the data from a molecule template to a molecule file.

The molecule file format is determined by the file name: if the file name ends in .json the file will be written in JSON format, otherwise the file is written in the native LAMMPS molecule file format.

When the molecule template contains multiple molecules, as defined by a molecule command with multiple molecule files, the filename must contain a ‘%’ character. That ‘%’ character will be replaced by the molecule number (starting from 1) and each molecule is written to a separate file.

Output Format

The output format follows the description of the molecule file format in the molecule command documentation. When parsing molecule files there are a few requirement about the order of sections for the native format, but generally the order of list entries can be chosen freely. On writing, however, a specific ordering is enforced following the lists given below. All sections with per-atom data are sorted by the atom-ID value starting from 1. The list of bonds is ordered by the atom-ID of the first atom in the bond. The lists of angles, dihedrals, and impropers are ordered by the atom-ID of the second atom in the definition. For entries with the same atom-ID, the order in which they were defined in the original input data is maintained.

Native Format

The native format starts with a title line similar to the following where the angular brackets are replaced with the actual data:

# MOLECULE <molecule-ID>, unit = <units setting>, set <set-ID> of <nsets>, <original title>

This followed by a header section with the following keywords in the listed order:

  • atoms (required keyword)

  • bonds (if non-zero)

  • angles (if non-zero)

  • dihedrals (if non-zero)

  • impropers (if non-zero)

  • fragments (if non-zero)

  • mass (if present in original input)

  • body (if present in original input)

  • com (if present in original input)

  • inertia (if present in original input)

The header section is followed by individual data sections in the order given below if the corresponding data was provided in the original input or explicitly added later:

  • Coords

  • Types

  • Molecules

  • Fragments

  • Charges

  • Diameters

  • Dipoles

  • Masses

  • Bonds

  • Angles

  • Dihedrals

  • Impropers

  • Special Bond Counts

  • Special Bonds

  • Shake Flags

  • Shake Atoms

  • Shake Bond Types

  • Body Integers

  • Body Doubles

JSON Format

The JSON output is written as a text file in strict JSON format with an indentation level of 2 and following the layout given in the JSON schema file available for download at https://download.lammps.org/json/molecule-schema.json

Unlike for the native format output, there is no need to provide any counts for the number of entries for keys containing lists of settings with a specified format, since those can be directly inferred from the data structures after parsing a JSON file. The top level keys are ordered as follows:

  • application

  • format

  • revision

  • schema

  • title

  • units

  • masstotal (if present in original input)

  • com (if present in original input)

  • inertia (if present in original input)

  • coords (if present in molecule data)

  • types

  • molecules (if present in molecule data)

  • fragments (if present in molecule data)

  • charges (if present in molecule data)

  • diameters (if present in molecule data)

  • dipoles (if present in molecule data)

  • masses (if present in molecule data)

  • bonds (if present in molecule data)

  • angles (if present in molecule data)

  • dihedrals (if present in molecule data)

  • impropers (if present in molecule data)

  • special (if present in original input)

  • shake (if present in molecule data)

  • body (if present in molecule data)

Restrictions

None

Defaults

None